Programme - M.Sc. Biotechnology: L T P/S SW/F W Total Credit Units 3 0 0 0 3

!
Programme – M.Sc. Biotechnology

L T P/S SW/F TOTAL
W CREDIT
UNITS
3 0 0 0 3
Course Title: Genomics and Proteomics

Course Code: GCMB701 Credit Units: 03
Course Objectives: The course aims to appraise the students to the vital concepts of technologies pertinent to Genomics and Proteomics, their applications
and demonstrate skills to apply the knowledge in scientific queries.
Prerequisite : Advanced Molecular Biology, Advanced Recombinant DNA Technology, Advanced Genetics and Bioinformatics & Computational Biology
Student Learning Outcomes: On the completion of the course

• The student will be able discern the crucial concepts and techniques applied in genomics, transcriptomics and proteomics.
• Be able to classify the complexity of genome/ proteome structural and functional organization.
• Formulate and assess experimental design for solving theoretical and experimental problems in Genomics and Proteomics fields.
Course Contents/Syllabus:
Weightage (%)
Module I 25
Descriptors/Topics - Genomes – Organization and sequencing
Genome evolution – Protogenomes, shift from RNA genome to DNA genome, Methods of acquisition of new genes
Genome organization - Organization of Prokaryotic and Eukaryotic Genomes, C – value paradox, Organelle genomes
and Endosymbiont theory
Sequencing Strategies – Whole Genome Shotgun and Hierarchical Shotgun, Genome Assembly – use of overlap,
physical maps, genetic maps, STS markers etc. reads, contigs, scaffolds; Finishing - physical and sequencing gaps,
methods to bridge gaps, Concepts of N-50, Genome coverage
Genome Annotation –Open Reading Frame, Codon bias, challenges in annotating a eukaryotic genome vs.
prokaryotic genomes, in silico annotation approaches – de novo, homology based annotation – gene finding algorithms
Human Genome - Organization of coding and non coding regions, findings and impact and of the human genome
Module II 15
Descriptors/Topics –DNA Sequencing Techniquesand applications

Second generation Sequencing techniques – Pyrosequencing, Virtual Terminator Sequencing, Introduction to third
generation Sequencing Techniques – Nanopore and Ion torrent, Applications - Personal Genomics, Metagenomics
Module III 10
Variations in genomes and Molecular markers –

Descriptors/Topics
Concepts, assays and Applications – Dominant and codominant markers, RFLP, AFLP, CAPS, SSRs, RAPDs, SNPs,
Copy number variations (CNVs), The histone code - Epigenetic variations; Conventional knockout approaches,
conditional knockouts, Current knockout approaches
Module IV 25
Descriptors/Topics - Conceptualizing
Functional Genomics, Trancriptomics and Proteomics
Concepts of forward and reverse genetics; Transcript Sequencing vs. Hybridization; Functional Genomics using RNAi;
High throughput transcriptomic techniques – Real Time analysis, Microarray, SAGE, RNASeq, ChIPSeq, The
ENCODE project; High-throughput Cloning and applications; Biological Networks
Module V 25
Descriptors/Topics – Scientific and Technological Applications of Proteomics techniques

Qualitative and quantitative proteome analysis; Proteome characterization techniques – 2D-gel electrophoresis, DIGE,
Mass Spectrometry – Concepts, Ionization (MALDI, ESI, Nanospray, Mass Analyzers – Time of Flight, Magnetic
sector, Quadrupole, Orbitrap; MS-MS approaches, Peptide Mass finger printing and Post Translational Modifications
Interactomics, Protein protein interaction assays - Two-hybrid methods, TAP/ GFP tags, Phage Display, Protein chips;
Proteome-wide interaction maps, Proteomics workflows ; Protein Engineering; An introduction to systems biology
Pedagogy for Course Delivery:
Lectures – 43
Class test – 2
Total – 45 hours
Assessment/ Examination Scheme:

Theory L/T (%) Lab/Practical/Studio (%) End Term Examination
100 - 100
Theory Assessment (L&T):

Continuous Assessment/Internal Assessment End Term
Examination
Components (Drop Class test I Assignment Viva Attendance
down)
Weightage (%) 15 5 5 5 70
Text & References:

• Discovering Genomics, Proteomics and Bioinformatics, 2nd Edition. Campbell AM & Heyer LJ, Benjamin Cummings 2007; CSH Press, NY.
ISBN-10: 8131715590
• Principles of Proteomics. R.M Twyman (2004). (BIOS Scientific publishers). ISBN-10: 1859962734
• Principles of Gene Manipulation and Genomics- Primrose S & Twyman R, 7th Edition, Blackwell, 2006. ISBN-10: 1405135441
• Principles of Genome Analysis and Genomics. Primrose SB & Twyman RM. 2007. Blackwell. ISBN-10: 1405101202
• Introduction to Genomics. A.M Lesk, Oxford University press, 2007. ISBN-10: 0199557489
• A Primer of Genome Science. Greg Gibson and Spencer V. Muse. 2nd ed. 2004. SINAUER Associates Inc. ISBN-10: 0878932364
• Genome III – T.A. Brown Garland Science Publ. June 08, 2006. ISBN-10: 0815341385
• Introduction to Proteomics: Tools for the New Biology. Daniel C. Liebler, Humana Press Inc., 2002. ISBN-10: 0896039919
• Bioinformatics – Sequence and Genome Analysis – David W. Mount –Cold Spring Harbor Laboratory Press, U.S.; 2nd Revised edition,
2004. ISBN-10: 9746520709
• Essential Bioinformatics – Xing Xiong – Cambridge University Press, New York, 2006. ISBN-10: 0521706106
• Bioinformatics and Functional Genomics – Jonathan Pevsner - 2nd edition, Wiley-Blackwell, 2009. ISBN-10: 0471210048
Any other Study Material:

• Proteomic to study genes and genomes (2000). Nature 405: 837-846.
• Application of DNA microarrays in Biology (2005) Ann. review of Biochemistry 74: 53-82.
• Functional Proteomics (2005) Clin Chim Acta 357: 140-150.
• Mass spectrometry for proteomics (2008), Curr Opin Chem Biol. Oct;12(5):483-90.
• ChIPSeq and beyond – Nature reviews Genetics Volume 13, 2012, 840-852
• Sequencing Technologies – The next Generation – Nature reviews Genetics Volume 11, 2010, 31-46
• Proteomics: Challenges, Techniques and Possibilities to Overcome Biological Sample Complexity – Human Genomics and Proteomics,2009. •
NCBI online tutorials and Videos
• Genome TV – You tube videos form NIH

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Programme – M.Sc. Biotechnology

Course Title: Genomics and Proteomics

Student Learning Outcomes: On the completion of the course

Descriptors/Topics –DNA Sequencing Techniquesand applications

Variations in genomes and Molecular markers –

Descriptors/Topics – Scientific and Technological Applications of Proteomics techniques

Assessment/ Examination Scheme:

Theory Assessment (L&T):

Text & References:

Any other Study Material:

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